[English] 日本語
Yorodumi
- PDB-6zwe: Crystal structure of human acetylcholinesterase in complex with (... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zwe
TitleCrystal structure of human acetylcholinesterase in complex with ((6-((2E,4E)-5-(benzo[d][1,3]dioxol-5-yl)penta-2,4-dienamido)hexyl)triphenylphosphonium bromide)
ComponentsAcetylcholinesterase
KeywordsHYDROLASE / human acetylcholinesterase / piperine derivative / mitochondria
Function / homology
Function and homology information


negative regulation of synaptic transmission, cholinergic / serine hydrolase activity / Neurotransmitter clearance / acetylcholine catabolic process in synaptic cleft / cholinesterase activity / acetylcholine catabolic process / acetylcholine binding / amyloid precursor protein metabolic process / acetylcholinesterase / acetylcholine receptor signaling pathway ...negative regulation of synaptic transmission, cholinergic / serine hydrolase activity / Neurotransmitter clearance / acetylcholine catabolic process in synaptic cleft / cholinesterase activity / acetylcholine catabolic process / acetylcholine binding / amyloid precursor protein metabolic process / acetylcholinesterase / acetylcholine receptor signaling pathway / osteoblast development / acetylcholinesterase activity / choline metabolic process / Synthesis of PC / basement membrane / regulation of receptor recycling / Synthesis, secretion, and deacylation of Ghrelin / laminin binding / side of membrane / synaptic cleft / synapse assembly / collagen binding / positive regulation of protein secretion / neuromuscular junction / receptor internalization / : / retina development in camera-type eye / nervous system development / positive regulation of cold-induced thermogenesis / amyloid-beta binding / hydrolase activity / cell adhesion / synapse / perinuclear region of cytoplasm / Golgi apparatus / cell surface / protein homodimerization activity / extracellular space / extracellular region / membrane / nucleus / plasma membrane
Similarity search - Function
Acetylcholinesterase, tetramerisation domain / Acetylcholinesterase tetramerisation domain / Cholinesterase / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
BROMIDE ION / Chem-QRH / Acetylcholinesterase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsDa Silva, O. / Dias, J. / Nachon, F. / Brazzolotto, X.
CitationJournal: Antioxidants (Basel) / Year: 2021
Title: Fine-Tuning the Biological Profile of Multitarget Mitochondriotropic Antioxidants for Neurodegenerative Diseases.
Authors: Chavarria, D. / Da Silva, O. / Benfeito, S. / Barreiro, S. / Garrido, J. / Cagide, F. / Soares, P. / Remiao, F. / Brazzolotto, X. / Nachon, F. / Oliveira, P.J. / Dias, J. / Borges, F.
History
DepositionJul 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Acetylcholinesterase
B: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,94950
Polymers118,8942
Non-polymers5,05548
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9820 Å2
ΔGint-340 kcal/mol
Surface area40140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)211.350, 211.350, 115.900
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'A' and (resid 5 through 363 or resid 365...A5 - 257
121(chain 'A' and (resid 5 through 363 or resid 365...A265 - 362
131(chain 'A' and (resid 5 through 363 or resid 365...A365 - 379
141(chain 'A' and (resid 5 through 363 or resid 365...A382 - 543
151(chain 'A' and (resid 5 through 363 or resid 365...A600 - 602
261(chain 'B' and (resid 5 through 258 or resid 265...B5 - 257
271(chain 'B' and (resid 5 through 258 or resid 265...B265 - 362
281(chain 'B' and (resid 5 through 258 or resid 265...B365 - 379
291(chain 'B' and (resid 5 through 258 or resid 265...B382 - 543
2101(chain 'B' and (resid 5 through 258 or resid 265...B600 - 602

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Acetylcholinesterase / / AChE


Mass: 59447.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACHE / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P22303, acetylcholinesterase

-
Sugars , 3 types, 4 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-3DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a3-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 5 types, 189 molecules

#5: Chemical ChemComp-QRH / (2~{E},4~{E})-5-(1,3-benzodioxol-5-yl)-~{N}-[6-(triphenyl-$l^{5}-phosphanyl)hexyl]penta-2,4-dienamide


Mass: 563.666 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H38NO3P / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#8: Chemical...
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 6.29 Å3/Da / Density % sol: 80.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.5 M LiSO4, 100 mM HEPES pH7, 60 mM MgSO4

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 3→78.09 Å / Num. obs: 59080 / % possible obs: 99.87 % / Redundancy: 39.8 % / Biso Wilson estimate: 85.22 Å2 / CC1/2: 0.999 / Net I/σ(I): 20.81
Reflection shellResolution: 3→3.107 Å / Num. unique obs: 5885 / CC1/2: 0.933

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EY4

4ey4


Resolution: 3→78.09 Å / SU ML: 0.3944 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 30.9732
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2423 1180 2 %
Rwork0.1977 57844 -
obs0.1985 59024 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 97.42 Å2
Refinement stepCycle: LAST / Resolution: 3→78.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8335 0 274 145 8754
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00438859
X-RAY DIFFRACTIONf_angle_d0.87112125
X-RAY DIFFRACTIONf_chiral_restr0.05781300
X-RAY DIFFRACTIONf_plane_restr0.00721581
X-RAY DIFFRACTIONf_dihedral_angle_d21.59181268
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.140.39241470.33427201X-RAY DIFFRACTION99.69
3.14-3.30.3441470.2847209X-RAY DIFFRACTION99.9
3.3-3.510.2681450.24867167X-RAY DIFFRACTION99.86
3.51-3.780.28971470.21587211X-RAY DIFFRACTION99.9
3.78-4.160.221470.19327202X-RAY DIFFRACTION99.96
4.16-4.760.22271480.16967235X-RAY DIFFRACTION99.97
4.76-60.20751480.18287267X-RAY DIFFRACTION100
6-78.090.22161510.17227352X-RAY DIFFRACTION99.73

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more